Search Results (79)

Long-term cultivation of strawberries can alter plant-associated microbial communities; however, the responses of root-associated bacteria within the combined rhizoplane and endophytic community remain insufficiently characterized. This study compared bacterial community composition, co-occurrence patterns, and predicted ecological functions in root-associated bacteria from short-term (4 months; 4 mon) and long-term (16 months; 16 mon) cultivation of Dandong 99 strawberry plants. Because the two groups differed simultaneously in soil cultivation history, plant age, and root developmental stage, all observed differences are interpreted as correlates of cultivation duration rather than as effects of continuous cropping per season. The 6 composite root samples were analyzed using Illumina NovaSeq sequencing of the bacterial 16S rRNA V4 region, followed by ASV-based diversity analysis, taxonomic profiling, LEfSe, FastSpar-based co-occurrence network analysis, and FAPROTAX functional prediction. Across all samples, 264,350 high-quality sequences and 11,442 ASVs were obtained. Long-term cultivation was associated with lower observed ASV richness and a marked shift in community composition (PERMANOVA R² = 0.935; ANOSIM R = 1). At the phylum level, Actinobacteria declined significantly (30.50% to 12.85%), while Proteobacteria and Bacteroidota were enriched. At the genus level, Streptomyces, Steroidobacter, Bradyrhizobium, and unidentified Rhizobiaceae decreased significantly. Network analysis identified Sphingobium, Bradyrhizobium, and Steroidobacter as highly connected genera by degree centrality, with the latter two also showing reduced relative abundance. Functional prediction indicated significantly lower predicted chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, nitrate reduction, and chitinolysis, alongside higher predicted methylotrophy, methanol oxidation, ureolysis, and aromatic compound degradation. These findings provide genus-level evidence that cultivation duration is associated with compositional and predicted functional shifts in strawberry root-associated bacteria. The depleted Actinobacteria and Bradyrhizobium partially align with microbial signatures of continuous cropping obstacles, warranting future validation in age-controlled, temporally replicated studies. Full article

The microbial fermentation of mulberry branch residues offers a potential strategy for sustainable lignocellulosic biomass valorization. This study integrated 16S rRNA gene sequencing and untargeted LC–MS metabolomics to characterize temporal microbial and metabolic changes during a 12-day solid-state fermentation at 35 °C using a defined consortium of lactic acid bacteria, Bacillus subtilis, and Saccharomyces cerevisiae. Microbial community analysis revealed distinct temporal succession, with Bacillus accounting for 19.5% of the bacterial community during early fermentation, followed by increasingly diverse assemblages. Exploratory machine learning analysis ranked Azotobacter and Kyrpidia among the genera contributing most strongly to temporal differentiation. FAPROTAX-based predictions indicated that chemoheterotrophy-related functions remained prevalent across fermentation stages, although these predictions do not represent direct functional activity. Untargeted metabolomics detected 2782 putatively annotated features, dominated by lipids (15.1%), organic acids (13.8%), and phenylpropanoids (13.2%). Correlation analysis identified temporal associations between bacterial genera and metabolite classes, including associations of Geobacillus with alkaloids and glycerophospholipids. Exploratory OPLS-DA further highlighted pseudouridine and 3-methylxanthine as discriminatory features across fermentation stages. These findings provide a descriptive multi-omics overview of microbial succession and metabolic variation during mulberry branch residue fermentation. Full article

Diflufenican is a herbicide widely used in agricultural systems, but its effects on soil bacterial communities across different soil depths remain insufficiently understood. In this study, we investigated depth-resolved bacterial community responses and functional potential following diflufenican perturbation in agricultural soils. Soil samples collected from different depths were incubated with or without diflufenican, and bacterial communities were analyzed using 16S rRNA gene amplicon sequencing. Co-occurrence network analysis was conducted to explore potential bacterial association patterns, and PICRUSt2 and FAPROTAX were used to infer bacterial functional potential. Diflufenican perturbation altered bacterial alpha diversity and reshaped community composition, with response patterns varying among soil depths. Principal coordinate analysis based on Bray–Curtis dissimilarity showed separation between control and diflufenican-treated soils, indicating treatment-associated shifts in bacterial community structure. Several genera, including Sphingomonas, Pseudarthrobacter, Bacillus, Microvirga, and Phenylobacterium, were enriched in diflufenican-treated soils, suggesting that they may represent candidate diflufenican-associated taxa. Co-occurrence network analysis further indicated changes in potential bacterial association patterns after diflufenican perturbation. Functional inference suggested shifts in bacterial functional potential, particularly in nutrient cycling-related functions, and these shifts differed among soil depths. Overall, these findings indicate that diflufenican perturbation reshapes soil bacterial community structure and alters inferred functional potential in a depth-dependent manner, highlighting the importance of soil vertical depth in assessing herbicide impacts on agricultural soil microbiomes. Full article

This study investigates earthworm cocoons as key vectors for the vertical transmission of symbiotic bacteria, a process that profoundly shapes the gut microbiota of offspring and influences their environmental adaptability. However, systematic knowledge of the internal microbiome communities within earthworm cocoons remains limited. Here, we characterized the composition and functional potential of bacterial communities within cocoons of earthworms collected from three composting systems (fermented coffee grounds, cow manure, and residual sludge) using high-throughput sequencing, together with diversity analyses, dominant taxa identification, and FAPROTAX-based functional prediction. Our results indicated that the composting system significantly affects bacterial diversity and community structure. The fermented coffee grounds system supported the highest species richness, whereas the cow manure system exhibited the greatest diversity and evenness. At the phylum level, Pseudomonadota, Actinomycetota, and Bacteroidota predominated across all systems, with Pseudomonadota being particularly abundant (62.01–81.41%). At the genus level, Verminephrobacter and Agromyces were consistently dominant, with Verminephrobacter showing particularly high relative abundance, ranging from 22.42% to 51.51%. Although the composition and abundance of dominant phyla and genera varied among systems, the shared OTUs accounted for a substantial proportion of the relative abundance in each sample (54.65–91.84%). Functional predictions revealed chemoorganoheterotrophy as the predominant metabolic function, with relative abundances ranging from 23.87% to 45.42%. Collectively, these findings provide insights into how composting environments shape the bacterial communities within earthworm cocoons, offering a theoretical foundation for understanding the ecological functions of earthworms and their potential applications in ecological restoration and sustainable agriculture. Full article

Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3–V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies. Full article

This study used 16S rDNA high-throughput sequencing and Faprotax functional prediction to analyze the effects of different artificial forests (coniferous forest, conifer–broad-leaved mixed forest, broad-leaved forest) in the Fanggan ecological restoration area of North China on soil bacterial community composition and functional characteristics and, based on network topology features, analyzed the potential influencing pathways. Planting broad-leaved forests significantly increased soil bacterial α-diversity indices (ACE, Chao1, Shannon) and induced the greatest heterogeneity in both community and functional composition. Soil bacteria exhibit significant differences in taxonomic structure across forest types but not in functional structure. The classification network and functional network of broad-leaved forests are more complex than those of coniferous and mixed forests, with the former having more nodes and edges, as well as higher weighted degree and betweenness centrality. Zi-Pi analysis indicates that high-abundance taxa involved in carbon and nitrogen cycles dominate the keystone taxa of the taxonomic network, while low-abundance pathogenic, urea-decomposing, and trace element metabolism functional groups dominate the keystone groups of the functional network. Redundancy analysis further revealed that soil available potassium concentration, pH, and tree species composition (importance values of Pinus tabulaeformis and Populus davidiana) were the principal determinants of bacterial functional structure. Collectively, broad-leaved forests achieve higher network robustness via elevated network complexity and functional redundancy, whereas coniferous forests might rely on functional convergence and modular integration to cope with resource limitation. These results indicate that network traits mediate the distinct responses of bacterial communities and their functional potentials, offering practical references for vegetation restoration in limestone mountain areas. Full article

Arbuscular mycorrhizal fungi (AMF) can improve plant performance, but how they coordinately influence root metabolism and associated bacterial communities in sweet potato remains unclear. Here, a pot experiment was conducted to investigate the effects of Glomus intraradices inoculation on sweet potato seedlings by integrating analyses of rhizosphere soil properties, plant growth and nutrient uptake, root metabolomics, and rhizosphere and endophytic bacterial communities using 16S rRNA gene sequencing with FAPROTAX-based functional prediction. AMF inoculation significantly increased whole-plant fresh and dry biomass, potassium concentration and accumulation, and the accumulation of starch and water-soluble carbohydrates, while no significant effects were observed on dry matter rate or plant nitrogen and phosphorus concentration. In the rhizosphere, AMF reduced soil electrical conductivity and increased organic matter content without significantly affecting pH, alkali-hydrolyzable nitrogen, available phosphorus, or available potassium. Root metabolomic profiling identified 289 differential metabolites, with enrichment of phenylpropanoid biosynthesis, glycerophospholipid metabolism, porphyrin metabolism, and nucleotide metabolism, together with broad up-regulation of lipid-related metabolites. Bacterial communities showed strong compartment specificity, with the root endosphere displaying lower alpha diversity than the rhizosphere. Higher rhizosphere bacterial Shannon diversity was observed in the AMF treatment, together with compartment-dependent shifts in bacterial community composition; enrichment of endophytic taxa such as Devosia and Niastella was detected following AMF inoculation. Functional prediction further suggested niche differentiation between rhizosphere and endophytic bacteria, together with AMF-associated shifts in carbon- and nitrogen-related functions. Overall, these results suggest that G. intraradices inoculation is associated with enhanced sweet potato growth and enhanced potassium and carbohydrate accumulation in association with coordinated changes in rhizosphere conditions, root metabolism, and bacterial community assembly. Full article

Microbial functional traits play a central role in regulating carbon mineralization efficiency (CME) in peatlands, yet how they respond to concurrent warming and atmospheric nitrogen deposition remains unclear. In this study, peat soils from three vegetation types (sedge, reed, and shrub) were subjected to controlled microcosm incubations simulating warming and nitrogen addition gradients. Microbial community composition and functional profiles were characterized using 16S rRNA high-throughput sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX) functional prediction, while dissolved organic matter (DOM) composition was analyzed via excitation–emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC) and fluorescence indices. Integrating correlation analysis, Random Forest, and partial least squares path modeling (PLS-PM) modeling, we identified microbial functional traits as key factors linking environmental changes to soil CME, with DOM serving as a substrate-mediated pathway. External nitrogen input primarily drove shifts in microbial functional composition, whereas warming modulated substrate utilization preferences and DOM turnover. The interaction between warming and nitrogen selectively reshaped microbial functional profiles, thereby jointly determining CME. Functional traits explained more variation in CME than taxonomic composition, indicating a “structure–function decoupling” under environmental change. These findings highlight the central role of microbial functional traits in peatland carbon transformation and suggest that the net response of peatland carbon emissions to future environmental change will depend critically on the balance between warming magnitude and nitrogen deposition levels. Full article

Organic amendments can mitigate soil acidification and degradation, yet their long-term effects on soil microbiome, functions, and crop productivity remain underexplored in latosolic red soils. This study aimed to elucidate how different fertilization regimes reshape soil microbial communities and predicted functions, and how these changes link to sweet potato productivity after 15 years. Soil and plant samples were collected from a 15-year field experiment on latosolic red soil under five treatments: no fertilizer (CK), chemical fertilizer alone (NPK), and chemical fertilizer combined with commercial manure (NPK + CM), pig manure (NPK + PM), or rice straw (NPK + RS). Soil properties, bacterial and fungal communities, and predicted functions (FAPROTAX, FUNGuild) were analyzed. The results showed that long-term NPK alone significantly acidified soil (pH decreased by 1.49 units), whereas NPK + PM increased pH by 1.38 units relative to NPK, and also increased soil organic carbon, available nutrients, and sweet potato yield (by 31% compared with NPK). Soil pH was strongly associated with reshaping the microbial community. NPK + PM enriched beneficial phyla (e.g., Myxococcota, Nitrospirota, Latescibacterota, Entotheonellaeota, and Mortierellomycota) and enhanced predicted chemoheterotrophic, predatory or exoparasitic, and saprotrophic functions. Variance partitioning showed that nutrients, key microbial taxa, and predicted functions jointly explained productivity variation (adjusted R² = 0.9386). Thus, chemical fertilizer combined with pig manure is an effective strategy to mitigate soil acidification and improve sweet potato productivity by regulating soil nutrient-microbiome interactions. Our findings support reshaping the microbiome via organic amendments for sustainable agriculture in acidic soils. Full article

Wetland degradation in soda saline–alkali ecosystems can profoundly alter belowground microbial communities, yet its effects on bacterial phylogenetic distribution and predicted ecological characteristics remain insufficiently understood. This study investigated soil physicochemical properties, enzyme activities, and bacterial communities across a wetland degradation gradient in the Halahai Provincial Nature Reserve, China, including reed wetland (RW), meadow steppe (MS), and degraded Suaeda saline patches (DS). Soil analyses were integrated with 16S rRNA gene amplicon sequencing, phylogenetic reconstruction, and FAPROTAX and BugBase prediction. DS showed significantly higher pH and electrical conductivity, but lower soil water content, organic carbon, nutrient availability, and urease activity than RW and MS. Alpha diversity analysis indicated that DS had lower bacterial richness and diversity, but higher dominance, whereas RW and MS did not differ significantly. Beta-diversity analysis revealed clear habitat-dependent separation, with DS harboring the most distinct community structure. Taxonomic and phylogenetic analyses indicated enrichment of Gemmatimonadota and the RCP2-54 lineage in DS, whereas RW and MS were more strongly associated with Pseudomonadota, Acidobacteriota, and related groups. Predicted functional and phenotypic analyses further suggested a shift toward stress-related and degradation-associated traits in DS. These findings demonstrate that wetland degradation reshaped the taxonomic composition, phylogenetic distribution, and predicted ecological characteristics of soil bacterial communities in this fragile ecosystem. Full article

This study investigated the effects of different breeding methods on the cecal microbiota and production traits of Yimeng Black Goats (YBGs). Twenty-seven 3-month-old male YBGs were assigned to three groups (n = 9 each): total mixed ration once daily (A), concentrate in the morning and roughage in the afternoon (B), or grazing with supplementary feeding (C). Cecal bacterial communities were analyzed via 16S rRNA sequencing, and functional potential was predicted using FAPROTAX. Breeding method significantly altered microbial composition (p < 0.05). Beta diversity was highest in Group C, while alpha diversity remained similar across groups. Bacteroidetes, Firmicutes, and Proteobacteria were dominant; Proteobacteria were most abundant in Group A. At the genus level, relative abundances of nine taxa, including Lactobacillus and Fusobacterium, differed significantly (p < 0.05). At the species level, including Lactobacillus mucosae, Bacteroides massiliensis and Alistipes finegoldii, differed significantly (p < 0.05). Chemoheterotrophy and fermentation functions were most enriched, particularly in Group C. Total weight gain was highest in Group A and lowest in Group C (p < 0.05), while carcass rate showed no significant differences (p > 0.05). Correlation analysis revealed that Proteobacteria, Fusobacteria, and Euryarchaeota as the key phylum, and Bacteroides, Tyzzerella, Fusobacterium, unidentified_Prevotellaceae, Methanovrevibacter and Faecalibacterium as the key genera were influencing the production traits of YBGs. These findings highlight the adaptive responses of the cecal microbiota to breeding methods and their potential links to host performance. Full article

Microcystin (MC) contamination of surface waters threatens ecosystems and public health. Nature-based solutions such as Multi-Soil-Layering (MSL) systems have been used for MC remediation. However, the biological mechanisms controlling MC degradation remain unclear. The present study investigates microbial community responses in two MSL systems with different clay contents (8% and 54%) exposed to MC-contaminated inputs (well water and eutrophied lake water). Samples were analysed before and after treatment using quantitative PCR (qPCR) to quantify the mlrA gene (encoding microcystinase) and its bacterial hosts. Next-generation sequencing (NGS) was used to assess microbial diversity, while the FAPROTAX database was used to predict functional characteristics. Results showed that MC was mainly adsorbed in pozzolan layers, while mlrA gene abundance and MC-degrading bacteria were higher in soil mixture layers. The presence of mlrA and associated bacteria was most pronounced in lake inflow samples, indicating intrinsic MC Biodegradation potential. Taxonomic analysis revealed dominant phyla including Proteobacteria, Actinobacteriota, Firmicutes, Chloroflexi and Bacteroidota. Functional analysis identified dominant traits such as chemoheterotrophy and aerobic metabolism. These findings provide new insights into microbial interactions in MSL systems and contribute to the optimisation of water treatment strategies for MC-contaminated environments. Full article

Saline–alkali soils significantly hinder agricultural productivity in China’s coastal areas. Although both plant growth-promoting rhizobacteria (PGPR) and biochar have individually demonstrated the capacity to boost crop yield and soil fertility, their synergistic effects on seawater rice and soil ecosystems remain uncertain. In this study, we examined the individual and interactive influences of lychee biochar (2.5% and 5% w/w) and PGPR inoculation on soil physicochemical properties and bacterial community assembly along a soil–root continuum, encompassing bulk soil, rhizosphere soil, rhizoplane, and root endosphere, in a controlled pot experiment with seawater rice. The application of biochar significantly altered soil pH, electrical conductivity, and nutrient availability in both bulk and rhizosphere soils, resulting in pronounced changes in bacterial community composition. The effects generated by biochar were partially mitigated when PGPR was co-applied. The relative abundances of Bacillota and Bacteroidota grew progressively from bulk soil to the root endosphere across all treatments, indicating a significant compartment-dependent selection. Co-occurrence network analysis and FAPROTAX-based functional predictions revealed several taxa and functions that were progressively enriched toward the root, including the halotolerant genera Exiguobacterium and Chryseobacterium, highlighting a significant host-mediated filtration process that functioned independently of the inoculated strains. Multivariate analyses further demonstrated that soil pH was the primary driver of bacterial community structure in bulk and rhizosphere soils, whereas plant-root selection dominated in the rhizoplane and endosphere. Overall, our results demonstrate that, within a seawater-rice and soil ecosystem, the selective influence of the host plant on root-associated microbiomes exceeds that of either biochar amendment or PGPR inoculation. This work improves our understanding of biochar–PGPR–plant interactions in saline–alkali soils and provides insight into sustainable strategies for enhancing rice production under salinity stress. Full article

Transport emissions are a major source of urban polycyclic aromatic hydrocarbons (PAHs), posing risks to human health. While plant leaves and their epiphytic microbes contribute to PAH degradation, how plant traits and environmental factors affect this process remains unclear. This study examined 20 tree species in Beijing’s traffic corridors to explore PAH enrichment on leaves and the structure of phyllospheric bacterial communities. Results show that leaf area, morphology, and sampling height significantly influenced bacterial community assembly. Normalized Stochasticity Ratio (NST) analysis indicated that deterministic processes dominate on medium-sized leaves (11.8–40.1 cm²), simple leaves, and those below 2.3 m or above 3 m in height, whereas stochastic factors prevail on nano leaves, compound leaves, and leaves at low-position (<2.3 m). Although low-molecular-weight PAHs (2–4 rings) were predominant in leaves, Mantel tests revealed significant positive correlations between bacterial communities and high molecular weight PAHs (4–6 rings), such as benz(a)anthracene, benzo[e]pyrene, and picene. Spearman analysis identified 10 dominant bacterial taxa with PAH degradation potential, including Kocuria rosea, Serratia symbiotica, Massilia sp. WG5, and seven unclassified species from Hymenobacter, Sphingomonas, Roseomonas, Curtobacterium, and Deinococcus. Functional Annotation of Prokaryotic Taxa(FAPROTAX) prediction further associated 14 species across six genera, including Acinetobacter, Nocardioides, Gordonia, Rhodococcus, Clostridium_sensu_stricto_18, and Geobacter, with PAH degradation function. This work clarifies the composition and function of phyllospheric PAH-degrading bacteria in an urban traffic environment, offering a theoretical basis for enhancing degradation via bacterial consortia, biosurfactants, and optimized plant selection. Full article

Arid and semi-arid soils represent extreme habitats where microbial life is constrained by high temperature, low water availability, salinity, and nutrient limitation, yet these ecosystems harbor unique bacterial communities that sustain key ecological processes. To explore the diversity and functional potential of prokaryotic assemblages in Algerian drylands, we compared soils from three contrasting sites: The Oasis of Djanet (RM1), the hyper-arid Tassili of Djanet desert (RM2), and the semi-arid El Ouricia forest in Sétif (RM3). Physicochemical analyses revealed strong environmental gradients: RM2 exhibited the highest pH (8.66), electrical conductivity (11.7 dS/m), and sand fraction (56%), whereas RM3 displayed the greatest moisture (10.9%), organic matter (7.6%), and calcium carbonate (20.7%) content, with RM1 generally showing intermediate levels. High-throughput 16S rRNA gene sequencing generated >60,000 effective reads per sample with sufficient coverage (>0.99). Alpha diversity indices indicated the highest bacterial richness and diversity in RM2 (Chao1 = 3144, Shannon = 10.0), while RM3 showed lower evenness and the dominance of a few taxa. Across sites, 66 phyla and 551 genera were detected, dominated by Actinobacteriota (38–45%) and Chloroflexi (13–44%), with Proteobacteria declining from RM1 (17.5%) to RM3 (3.3%). Venn analysis revealed limited overlap, with only 58 operational taxonomic units shared among all sites, suggesting highly habitat-specific communities. Predictive functional profiling (PICRUSt2, Tax4Fun, FAPROTAX) indicated metabolism as the dominant functional category (≈50% of KEGG Level-1), with carbohydrate and amino acid metabolism forming the metabolic backbone. Notably, transport functions (ABC transporters), lipid metabolism, and amino acid degradation pathways were enriched in RM2–RM3, consistent with adaptation to osmotic stress, nutrient limitation, and energy conservation under aridity. Collectively, these findings demonstrate that Algerian arid and semi-arid soils host diverse, site-specific bacterial communities whose functional repertoires are strongly shaped by soil chemistry and climate, highlighting their ecological and biotechnological potential. Full article